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    <title>Seq-QC</title>
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    <h1>
      <strong>Seq-QC : pSEVA uses PRINSEQ for sequence QC. </strong>
    </h1>
    <hr>
    <p>
      <img height="32" width="204" src="prinseq_logo_1.png"/>
    </p>
    <p>
      PRINSEQ is a tool that generates summary statistics of sequence and
      quality data and that is used to filter, reformat and trim next-generation
      sequence data. It is particular designed for 454/Roche data, but can also
      be used for other types of sequence data. PRINSEQ is available through a
      user-friendly web interface or as standalone version. The standalone
      version is primarily designed for data preprocessing and does not generate
      summary statistics in graphical form.
    </p>
    <p>
      PRINSEQ is distributed under the GNU Public License (GPL). All its source
      codes are freely available to both academic and commercial users. The
      latest version can be downloaded at the SourceForge download page. 
    </p>
   
    <!--  h:panelGroup style="background-color:Silver; border-color:Black;"-->
      <form method="post" enctype="multipart/form-data" action="prinseq.jsp">
      <p>
      <strong>Input Options: Select your input file format</strong>
      </p>
      <p>
        <select name="InputOptions">
          <option value="fastq"> fastq<option/>
          <option value="fasta"> fasta<option/>
          <option value="qual"> qual<option/>
        </select>
        &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<input type="file" size="80" name="InputFile">
      </p>
      <p>
        <strong>
          Output Options: Select your output file format</strong>
      </p>
      <p>
        <select name="OutputOptions">
          <option value="fastq"> fastq<option/>
          <option value="fasta"> fasta<option/>
          <option value="qual"> qual<option/>
        </select>
        &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<input type="file" size="80" name="OutputFile"/>
      </p>
      <p>
        <strong>Filter Options : Select filter options if you want to filter your input sequences.</strong>
      </p>
      <p>
        <input type="checkbox" name="Length" value="length"/>Length
      </p>
      <p>
        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;min &nbsp;&nbsp;&nbsp;<input type="text" size="10" name="LengthMax"/>
        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;range &nbsp;&nbsp;&nbsp;<input type="text" size="10" name="LengthRange"/>
      </p>
      <p>
        <input type="checkbox" name="GCContent" value="gccontent"/>GC content
      </p>
      <p>
        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;min &nbsp;&nbsp;&nbsp;<input type="text" size="10" name="GCcontentMin"/>
         &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;max &nbsp;&nbsp;<input type="text" size="10" name="GCContentMax"/>
         &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;range 
        <input type="text" size="10" name="GCContentRange"/>
      </p>
      <p>
        <input type="checkbox" name="QualScore"/>Quality score
      </p>
      <p>
        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;min &nbsp;&nbsp;&nbsp;<input type="text" size="10"/>
         &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;max &nbsp;&nbsp;<input type="text" size="10"/>
      </p>
      <p>
        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;min&nbsp;qual&nbsp;mean 
        <input type="text" size="10"/>
         &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;max&nbsp;qual&nbsp;mean 
        <input type="text" size="10"/>
      </p>
      <p>
        <input type="checkbox" name="numberofns"/>Number of Ns
      </p>
      <p>
        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;max(%) &nbsp;&nbsp;&nbsp;<input type="text" size="10"/>
         &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;max(num) &nbsp;&nbsp;<input type="text" size="10"/>
      </p>
      <p>
        <input type="checkbox" name="nonIUPAC"/>Non IUPAC
      </p>
      <p>
        <input type="checkbox" name="numberofseq"/>Number of Sequences&nbsp;&nbsp;&nbsp;&nbsp;<input type="text" size="10" name="NumberofSeq"/>
      </p>
      <p>
        <input type="checkbox" name="lowcomplexity"/>Low complexity
      </p>
      <p>
         &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;method 
        <select name="LC">
          <option value="dust"> dust</option>
          <option value="entropy"> entropy</option>
        </select>
        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;threshold &nbsp;&nbsp;&nbsp;<input type="text" size="10" name="threshold"/>
      </p>
      <p>

        <strong>Trim Options : Select trim options if you want to trim your input sequences.</strong>
      </p>
      <p>
        &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;length &nbsp;&nbsp;&nbsp;<input type="text" size="10" name="length"/>
         &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;left &nbsp;&nbsp;<input type="text" size="10"name="left"/>
         &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;right <input type="text" size="10" name="right"/>
      </p>
      <p>
        &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;tail&nbsp;left &nbsp;&nbsp;&nbsp;<input type="text" size="10" name="tailleft"/>
         &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;tail&nbsp;right&nbsp;&nbsp;<input type="text" size="10" name="tailright"/>
      </p>
      <p>
        &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;qual&nbsp;left &nbsp;&nbsp;&nbsp;<input type="text" size="10" name="qualleft"/>
         &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;qual&nbsp;right &nbsp;&nbsp;<input type="text" size="10" name="qualright"/>
      </p>
      <p>
         &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;qual&nbsp;type 
        <select name="QType">
          <option value="min" >qtypemin</option>
          <option value="mean" >qtypemean</option>
          <option value="max" >qtypemax</option>
          <option value="sum" >qtypesum</option>
        </select>
      </p>
      <p>
         &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;qual&nbsp;type 
        <select name="QRule">
          <option value="lt" >qrulelt</option>
          <option value="gt" >qrulegt</option>
          <option value="et" >qruleet</option>
        </select>
      </p>
      <p>
        &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;qual window &nbsp;&nbsp;&nbsp;<input type="text" size="10" name="qualwindow"/>
         &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;qual step &nbsp;&nbsp;<input type="text" size="10" name="qualstep"/>
      </p>
      
        <strong>Reformat : Select reformat options if you want to reformat your input sequences.</strong>
      <p>
         &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;qual&nbsp;Case 
        <select name="SeqCase">
          <option value="upper" >sequpper</option>
          <option value="lower" >seqlower</option>
        </select>
      </p>
      <p>
         &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;qual&nbsp;DNA/RNA 
        <select name="DNARNA">
          <option value="DNA" >dna</option>
          <option value="RNA" >rna</option>
        </select>
      </p>
      <p>
        &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;line width &nbsp;&nbsp;&nbsp;<input type="text" size="10" name="linewidth"/>
      </p>
       <p>
        <input type="checkbox" name="RmHeader"/>remove header
      </p>     
      <p>
        &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;sequence id &nbsp;&nbsp;&nbsp;<input type="text" size="10" name="sequenceid"/>
      </p>

         <strong>Summary statistics : Select summary statistics options if you want to see summary statistics of your input sequences.</strong>
      <p>
        <input type="checkbox" name="StatsInfo"/>basic information
      </p>     
      <p>
        <input type="checkbox" name="StatsLen"/>length information
      </p>     
      <p>
        <input type="checkbox" name="StatsDinuc"/>dinucleotide information
      </p>     
      <p>
        <input type="checkbox" name="StatsTag"/>the probability of a tag sequence
      </p>     
      <p>
        <input type="checkbox" name="StatsDupl"/>the number of exact duplicates
      </p>     
      <p>
        <input type="checkbox" name="StatsNs"/>the number of reads with N
      </p>     
      <p>
        <input type="checkbox" name="StatsAll"/>All available summary statistics
      </p>     

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